Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 13 of 13
Found at i:2508556 original size:19 final size:19
Alignment explanation
Indices: 2508534--2508668 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
2508524 GAAACCAAAA
*
2508534 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2508553 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2508569 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2508586 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2508602 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2508619 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2508638 TCTCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2508658 TCGTGTTGCGA
1 TCGCGTTGCGA
2508669 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 11 0.12
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2508575 original size:14 final size:14
Alignment explanation
Indices: 2508556--2508612 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2508546 TTTCATTTCG
2508556 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2508570 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2508587 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2508603 CGTTGCGATT
1 CGTTGCGATT
2508613 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2508581 original size:33 final size:33
Alignment explanation
Indices: 2508539--2508631 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2508529 CAAAATCGCA
*
2508539 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2508572 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2508605 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2508632 TTGGTTTCTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2510526 original size:38 final size:38
Alignment explanation
Indices: 2510483--2510555 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
2510473 TAATTGATTG
*
2510483 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
2510521 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
2510556 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:2510542 original size:19 final size:19
Alignment explanation
Indices: 2510479--2510542 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
2510469 AGTTTAATTG
2510479 ATTG-TTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
2510497 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
2510515 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
2510535 ATTGATTT
1 ATTGATTT
2510543 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 12, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
18 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:2510556 original size:14 final size:14
Alignment explanation
Indices: 2510537--2510572 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2510527 ATTGTTTAAT
2510537 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2510551 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2510565 TGATTTGT
1 TGATTTGT
2510573 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2510695 original size:19 final size:19
Alignment explanation
Indices: 2510679--2510779 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
2510669 AAAAATGACT
2510679 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2510698 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2510717 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2510731 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
2510749 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2510769 ATCGCAATGCG
1 ATCGCAATGCG
2510780 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 34 0.47
20 12 0.16
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2510826 original size:52 final size:52
Alignment explanation
Indices: 2510786--2511105 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
2510776 TGCGTTTATA
*
2510786 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2510838 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2510890 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2510947 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2510999 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2511051 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2511104 AT
1 AT
2511106 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2510832 original size:19 final size:19
Alignment explanation
Indices: 2510808--2511133 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
2510798 GATTATCTCG
2510808 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2510827 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2510846 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2510860 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2510879 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2510898 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
2510917 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
2510936 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2510955 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2510969 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2510988 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2511007 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2511021 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2511040 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2511059 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2511073 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2511093 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2511107 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2511126 TTGCGATT
1 TTGCGATT
2511134 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2511051 original size:161 final size:157
Alignment explanation
Indices: 2510786--2511105 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
2510776 TGCGTTTATA
2510786 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
2510851 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
2510916 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
2510947 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
2511012 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
2511077 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
2511104 AT
1 AT
2511106 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:2511077 original size:33 final size:33
Alignment explanation
Indices: 2510827--2511133 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
2510817 TCATTTCGCA
*
2510827 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2510860 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
2510896 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
2510934 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2510969 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
2511005 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
2511040 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2511073 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
2511107 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2511134 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2513455 original size:12 final size:12
Alignment explanation
Indices: 2513438--2513462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2513428 TCTTCGGGGA
2513438 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2513450 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2513462 C
1 C
2513463 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2513671 original size:24 final size:24
Alignment explanation
Indices: 2513637--2513683 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2513627 CTGAAACATC
2513637 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2513661 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2513684 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2514383 original size:20 final size:20
Alignment explanation
Indices: 2514355--2514723 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
2514345 AAATTTCAGT
* * * *
2514355 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2514375 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2514395 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2514415 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2514435 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2514455 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2514475 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2514495 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2514515 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2514535 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
* *
2514555 GTTGCGGTTTAAGGATACGC
1 GTTGCGATTTACGGATACGC
2514575 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2514595 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2514615 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2514635 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2514655 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2514675 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2514695 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2514715 GTTGCGATT
1 GTTGCGATT
2514724 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2530924 original size:2 final size:2
Alignment explanation
Indices: 2530919--2530957 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2530909 ATTAAAAAAC
2530919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2530958 ATTATACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2531787 original size:146 final size:147
Alignment explanation
Indices: 2531514--2531800 Score: 560
Period size: 145 Copynumber: 2.0 Consensus size: 147
2531504 AGCAATCTCC
2531514 CAAAAATCCGGTCTAAATCGGATTTAAATTGACTTCCTAATTAACAATCGAAATATTACCATAAA
1 CAAAAATCCGGTCTAAATCGGATTTAAATTGACTTCCTAATTAACAATCGAAATATTACCATAAA
2531579 TAGTAAAAAATAACTAAATCTAGTGATTCGGAGGAGAAAACGGCAGAATTTGAGGTTGAAAAAAA
66 TAGTAAAAAATAACTAAATCTAGTGATTCGGAGGAGAAAACGGCAGAATTTGAGGTTGAAAAAAA
2531644 GGCCACATAGAGAGCGT
131 GGCCACATAGAGAGCGT
2531661 CAAAAATCCGGTCTAAATC-GATTTAAATTGACTTCCTAATTAACAATCGAAATATTACCATAAA
1 CAAAAATCCGGTCTAAATCGGATTTAAATTGACTTCCTAATTAACAATCGAAATATTACCATAAA
2531725 TAGT-AAAAATAACTAAATCTAGTGATTCGGAGGAGAAAACGGCAGAATTTGAGGTTGAAAAAAA
66 TAGTAAAAAATAACTAAATCTAGTGATTCGGAGGAGAAAACGGCAGAATTTGAGGTTGAAAAAAA
2531789 GGCCACATAGAG
131 GGCCACATAGAG
2531801 CGTAGCTCAA
Statistics
Matches: 140, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
145 72 0.51
146 49 0.35
147 19 0.14
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (147 bp):
CAAAAATCCGGTCTAAATCGGATTTAAATTGACTTCCTAATTAACAATCGAAATATTACCATAAA
TAGTAAAAAATAACTAAATCTAGTGATTCGGAGGAGAAAACGGCAGAATTTGAGGTTGAAAAAAA
GGCCACATAGAGAGCGT
Found at i:2532387 original size:2 final size:2
Alignment explanation
Indices: 2532380--2532417 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2532370 TCCAAACAAC
2532380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2532418 CACTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2539869 original size:32 final size:33
Alignment explanation
Indices: 2539828--2539890 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2539818 TTGGGGCACC
*
2539828 TTTGAAGATTCAACATCAAATGTTGGGGCATTT
1 TTTGAAGATTCAACATCAAATATTGGGGCATTT
*
2539861 TTTG-AGATTCAACATCGAATATTGGGGCAT
1 TTTGAAGATTCAACATCAAATATTGGGGCAT
2539891 CTTCGGGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (33 bp):
TTTGAAGATTCAACATCAAATATTGGGGCATTT
Found at i:2539902 original size:32 final size:32
Alignment explanation
Indices: 2539817--2539904 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 32
2539807 ATGAGGAACA
* * *
2539817 ATTGGGGCACCTTTGAAGATTCAACATCAAAT
1 ATTGGGGCATCTTCGGAGATTCAACATCAAAT
* * ** *
2539849 GTTGGGGCATTTTTTGAGATTCAACATCGAAT
1 ATTGGGGCATCTTCGGAGATTCAACATCAAAT
*
2539881 ATTGGGGCATCTTCGGGGATTCAA
1 ATTGGGGCATCTTCGGAGATTCAA
2539905 AATCTTGATG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (32 bp):
ATTGGGGCATCTTCGGAGATTCAACATCAAAT
Found at i:2540407 original size:37 final size:38
Alignment explanation
Indices: 2540356--2540435 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 38
2540346 GTTTTTCTTA
* *
2540356 AAACAAGAATTTTGTCTCGCTTGAGATAGTTTCCCTTG
1 AAACAAGAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
*
2540394 AAACAA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAGAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
2540431 AAACA
1 AAACA
2540436 TAAACATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 33 0.85
38 6 0.15
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (38 bp):
AAACAAGAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
Found at i:2540498 original size:36 final size:37
Alignment explanation
Indices: 2540451--2540877 Score: 127
Period size: 36 Copynumber: 12.4 Consensus size: 37
2540441 ATTGAAAACA
**
2540451 TTTCCCTTGAAA-TGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCT-TTGAGATAG
*
2540487 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGA-CG
1 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGATAG
* * * *
2540523 ATTTCTCTTGAAACATAAA---------CATTGA-AAACA
1 -TTTCCCTTGAAACA-AAATTTTGTCTCCTTTGAGATA-G
2540553 TTTCCCTT-AAA-AATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAA--AATTTTGTCTCCT-TTGAGATAG
* *
2540590 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGATAG
* * * * *
2540626 TTTCTCTTGAAATATAAA---------CATTGA-AAACA
1 TTTCCCTTGAAACA-AAATTTTGTCTCCTTTGAGATA-G
**
2540655 TTTCCCTTGAAA-TGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCT-TTGAGATAG
* *
2540691 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGATAG
* *
2540727 TTTCTCTTGAAACAAAA-------T-CTTTGA-ATGTG
1 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGAT-AG
* * * *
2540756 TTTTCCTTGAAAC-AAATTTCGTCT-CTCTTGAGACAT
1 TTTCCCTTGAAACAAAATTTTGTCTCCT-TTGAGATAG
* *
2540792 TTTCTCC-TGAAAC-AAGTTTTGTCT-CTCTTGAGACAG
1 TTTC-CCTTGAAACAAAATTTTGTCTCCT-TTGAGATAG
* * *
2540828 TTTCCCTTGAAAC-GAATTTTGTCT-CTCTGGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCT-TTGAGATAG
*
2540864 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2540878 CCAATCTTTG
Statistics
Matches: 297, Mismatches: 44, Indels: 99
0.68 0.10 0.22
Matches are distributed among these distances:
26 1 0.00
27 3 0.01
28 12 0.04
29 45 0.15
30 1 0.00
35 6 0.02
36 164 0.55
37 51 0.17
38 14 0.05
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGATAG
Found at i:2540645 original size:204 final size:202
Alignment explanation
Indices: 2540360--2540840 Score: 727
Period size: 204 Copynumber: 2.4 Consensus size: 202
2540350 TTCTTAAAAC
*
2540360 AAGAATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTT
1 AAGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTT
2540425 CTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTT
65 CTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTT
*
2540490 CCCTTGAAACAAAATTTTGTCTCCTTTGAGAC-GATTTCTCTTGAAACATAAA-CATTGAAAACA
130 CCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG-TTTCTCTTGAAACA-AAATCATTGAAAACA
2540553 TTTCCCTTAAA
192 TTTCCCTTAAA
2540564 AATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
1 AA-GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
*
2540629 CTCTTGAAATATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTT
65 CTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTT
* ****
2540694 CCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATGTGTTT
130 CCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAAAACATTT
*
2540759 TCCTTGAAA
195 CCCTT-AAA
* * * * * *
2540768 CA-AATTTCGTCTCTCTTGAGACATTTTCTCC-TGAAACAAGTTTTGTCTCTCTTGAGACAGTTT
1 AAGAATTTTGTCTCTCTTGAGATAGTTTC-CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
*
2540831 CCCTTGAAAC
65 CTCTTGAAAC
2540841 GAATTTTGTC
Statistics
Matches: 255, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
202 64 0.25
203 49 0.19
204 107 0.42
205 35 0.14
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (202 bp):
AAGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
TCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTC
CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAAAACATTTC
CCTTAAA
Found at i:2540717 original size:101 final size:101
Alignment explanation
Indices: 2540362--2540840 Score: 721
Period size: 101 Copynumber: 4.7 Consensus size: 101
2540352 CTTAAAACAA
*
2540362 GAATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCT
2540427 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
65 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
*
2540464 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGAC-GATTTC
1 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG-TTTC
*
2540528 TCTTGAAACATAAACATTGAAAACATTTCCCTTAAAAAT
64 TCTTGAAACATAAACATTGAAAACATTTCCCTT-GAAAT
2540567 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
1 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
*
2540632 TTGAAATATAAACATTGAAAACATTTCCCTTGAAAT
66 TTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
2540668 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
1 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
* **** * *
2540733 TTGAAACA-AAATCTTTGAATGTGTTTTCCTTGAAAC
66 TTGAAACATAAA-CATTGAAAACATTTCCCTTGAAAT
* * * * * * *
2540769 AAATTTCGTCTCTCTTGAGACATTTTCTCC-TGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCC
1 GAATTTTGTCTCTCTTGAGATAGTTTC-CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
2540833 CTTGAAAC
65 CTTGAAAC
2540841 GAATTTTGTC
Statistics
Matches: 351, Mismatches: 21, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
100 3 0.01
101 156 0.44
102 151 0.43
103 41 0.12
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (101 bp):
GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
TTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
Found at i:2540977 original size:33 final size:33
Alignment explanation
Indices: 2540933--2540999 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2540923 ACATAAAAAG
*
2540933 AAACCTCTGAAATTGTTTATCTTGAAACACAAA
1 AAACCTCTGAAAATGTTTATCTTGAAACACAAA
* *
2540966 AAACCTTTGAAAATGTTTCTCTTGAAACACAAA
1 AAACCTCTGAAAATGTTTATCTTGAAACACAAA
2540999 A
1 A
2541000 CATTTGAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (33 bp):
AAACCTCTGAAAATGTTTATCTTGAAACACAAA
Found at i:2541006 original size:31 final size:32
Alignment explanation
Indices: 2540940--2541025 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 32
2540930 AAGAAACCTC
* *
2540940 TGAAATTGTTTATCTTGAAACACAAAAAACCTT
1 TGAAATTGTTTCTCTTGAAACAC-AAAAACATT
*
2540973 TGAAAATGTTTCTCTTGAAACAC-AAAACATT
1 TGAAATTGTTTCTCTTGAAACACAAAAACATT
* * *
2541004 TGAGATTGTTTCCCTCGAAACA
1 TGAAATTGTTTCTCTTGAAACA
2541026 AATTTTGTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 25 0.54
33 21 0.46
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
TGAAATTGTTTCTCTTGAAACACAAAAACATT
Found at i:2541059 original size:67 final size:67
Alignment explanation
Indices: 2540980--2541109 Score: 185
Period size: 67 Copynumber: 1.9 Consensus size: 67
2540970 CTTTGAAAAT
*
2540980 GTTTCTCTTGAAACACAAAA-CATTTGAGATTGT-T-TCCCTCGAAACAAATTTTGTCTCCCTTG
1 GTTTCTCTTGAAACACAAAATC-TTTGA-ATT-TATCTCCCTCAAAACAAATTTTGTCTCCCTTG
2541042 ATACA
63 ATACA
* *
2541047 GTTTCTCTTGAAACACAAAATCTTTGAATTTATCTCCCTTAAAACAAATTTTGTTTCCCTTGA
1 GTTTCTCTTGAAACACAAAATCTTTGAATTTATCTCCCTCAAAACAAATTTTGTCTCCCTTGA
2541110 AGCAACAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
65 1 0.02
66 4 0.07
67 51 0.89
68 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAATTTATCTCCCTCAAAACAAATTTTGTCTCCCTTGATA
CA
Found at i:2541139 original size:54 final size:52
Alignment explanation
Indices: 2541047--2541147 Score: 123
Period size: 54 Copynumber: 1.9 Consensus size: 52
2541037 CCTTGATACA
* *
2541047 GTTTCTCTTGAAACACAAAATCTTTGAATTTATCTCCCTTAAAACAAATTTT
1 GTTTCCCTTGAAACACAAAATCTTTGAATTCATCTCCCTTAAAACAAATTTT
* * *
2541099 GTTTCCCTTGAAGCAACAAATATCTTTGAGA-TCATTTCCCTTGAAACAA
1 GTTTCCCTTGAAAC-ACAAA-ATCTTTGA-ATTCATCTCCCTTAAAACAA
2541148 GTTCTGTCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 12 0.29
53 5 0.12
54 23 0.56
55 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.37
Consensus pattern (52 bp):
GTTTCCCTTGAAACACAAAATCTTTGAATTCATCTCCCTTAAAACAAATTTT
Found at i:2541653 original size:106 final size:107
Alignment explanation
Indices: 2541462--2541713 Score: 337
Period size: 106 Copynumber: 2.4 Consensus size: 107
2541452 GGTTTTAGCT
*
2541462 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
* ** **
2541527 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTT
66 CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAATTCC
* * * * *
2541568 GGAGCCAATTTCAACTTCACATCGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
* *
2541633 CGAAGGGACGACTGACTGTCAACAAAACAATTTCCTAGTTCC
66 CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAATTCC
* * *
2541675 AGAACCAATTTCAACTTCACGACAGAA-GATATTGGACTC
1 AGAGCCAATTTCAACTTCACAAC-GAAGGACATTGGACTC
2541714 GGAACAGCAC
Statistics
Matches: 125, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
106 79 0.63
107 43 0.34
108 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGACTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:2544426 original size:21 final size:21
Alignment explanation
Indices: 2544401--2544440 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2544391 AAAACAAAAA
* *
2544401 TCCATTCACCAGAAAAACTCT
1 TCCATGCAACAGAAAAACTCT
*
2544422 TCCATGCAAGAGAAAAACT
1 TCCATGCAACAGAAAAACT
2544441 ACACCAACTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (21 bp):
TCCATGCAACAGAAAAACTCT
Found at i:2555122 original size:30 final size:30
Alignment explanation
Indices: 2555088--2555183 Score: 174
Period size: 30 Copynumber: 3.2 Consensus size: 30
2555078 TTTTAATACA
2555088 GTCCCCAACATTTAGTTTGTTTGCAATATG
1 GTCCCCAACATTTAGTTTGTTTGCAATATG
2555118 GTCCCCAACATTTAGTTTGTTTGCAATATG
1 GTCCCCAACATTTAGTTTGTTTGCAATATG
* *
2555148 GTCCCCAACATTTAGTTTGTTTACAATATA
1 GTCCCCAACATTTAGTTTGTTTGCAATATG
2555178 GTCCCC
1 GTCCCC
2555184 GATGTAATCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (30 bp):
GTCCCCAACATTTAGTTTGTTTGCAATATG
Found at i:2557199 original size:31 final size:30
Alignment explanation
Indices: 2557127--2557199 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2557117 CAGTTACGTC
* *
2557127 GGGGACCATATTGCAAACGGACTAAATGTT
1 GGGGACCGTATTGCAAACGGACTAAATATT
* *
2557157 GGGGACCGTATTGTAAATGGACTAAATATT
1 GGGGACCGTATTGCAAACGGACTAAATATT
*
2557187 AGGGGACTGTATT
1 -GGGGACCGTATT
2557200 ACAAGTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (30 bp):
GGGGACCGTATTGCAAACGGACTAAATATT
Found at i:2558722 original size:25 final size:24
Alignment explanation
Indices: 2558696--2558740 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2558686 TTTTAATATA
*
2558696 TATACTTTTTAT-TAAAATTTATG
1 TATAATTTTTATATAAAATTTATG
*
2558719 TATAATTTTTTTATAAAATTTA
1 TATAATTTTTATATAAAATTTA
2558741 AAAGATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TATAATTTTTATATAAAATTTATG
Found at i:2565907 original size:2 final size:2
Alignment explanation
Indices: 2565900--2565936 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2565890 TTTAGGAAAT
2565900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2565937 TCAATTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2570469 original size:15 final size:16
Alignment explanation
Indices: 2570437--2570469 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2570427 AAAATCTTTC
2570437 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
2570453 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
2570468 TT
1 TT
2570470 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:2571243 original size:16 final size:16
Alignment explanation
Indices: 2571219--2571252 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2571209 TATCGCCGAC
*
2571219 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2571235 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2571251 CG
1 CG
2571253 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2576072 original size:37 final size:36
Alignment explanation
Indices: 2576013--2576164 Score: 191
Period size: 36 Copynumber: 4.2 Consensus size: 36
2576003 TGAATAAGAA
* *
2576013 GAACGAAAGAAAGCATC-ACACTTTCGATTCAAATT
1 GAACGGAAGAAAGCATCGACACTTTCGATTCAAATC
* *
2576048 GAAACGGAAGAAAACATCGACACTTCCGATTCAAATC
1 G-AACGGAAGAAAGCATCGACACTTTCGATTCAAATC
* * *
2576085 GAACGGAAGGAGGCATCGGCACTTTCGATTCAAATC
1 GAACGGAAGAAAGCATCGACACTTTCGATTCAAATC
* *
2576121 GAACAGAAGGAAGCATCGACAC-TTCTGATTCAAATC
1 GAACGGAAGAAAGCATCGACACTTTC-GATTCAAATC
2576157 GAACGGAA
1 GAACGGAA
2576165 AGATGTATCG
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
35 4 0.04
36 80 0.79
37 17 0.17
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (36 bp):
GAACGGAAGAAAGCATCGACACTTTCGATTCAAATC
Found at i:2576113 original size:73 final size:71
Alignment explanation
Indices: 2576025--2576182 Score: 217
Period size: 72 Copynumber: 2.2 Consensus size: 71
2576015 ACGAAAGAAA
* * *
2576025 GCATCACACTTTCGATTCAAATTGAAACGGAAGAAAACATCGACACTTCCGATTCAAATCGAACG
1 GCATCGCACTTTCGATTCAAATCG-AACAGAAGAAAACATCGACACTTCCGATTCAAATCGAACG
*
2576090 GAAGGAG
65 GAAAGAG
* * *
2576097 GCATCGGCACTTTCGATTCAAATCGAACAGAAGGAAGCATCGACACTTCTGATTCAAATCGAACG
1 GCATC-GCACTTTCGATTCAAATCGAACAGAAGAAAACATCGACACTTCCGATTCAAATCGAACG
*
2576162 GAAAGAT
65 GAAAGAG
*
2576169 GTATCGCACTTTCG
1 GCATCGCACTTTCG
2576183 TTTCGGGTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
71 9 0.12
72 50 0.66
73 17 0.22
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (71 bp):
GCATCGCACTTTCGATTCAAATCGAACAGAAGAAAACATCGACACTTCCGATTCAAATCGAACGG
AAAGAG
Found at i:2580602 original size:22 final size:22
Alignment explanation
Indices: 2580574--2580616 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2580564 AATTATAATT
**
2580574 TTAAATTGTGGATACGTTTACA
1 TTAAATTGTACATACGTTTACA
2580596 TTAAATTGTACATACGTTTAC
1 TTAAATTGTACATACGTTTAC
2580617 GATATCCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (22 bp):
TTAAATTGTACATACGTTTACA
Found at i:2582337 original size:27 final size:26
Alignment explanation
Indices: 2582283--2582341 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2582273 TTTTCTTCGA
*
2582283 TATTGAAAAATAAATATTAAAATAATT
1 TATT-AAAAATAAATATAAAAATAATT
* *
2582310 TATTAAAAATATATATAAATAATTATT
1 TATTAAAAATAAATATAAA-AATAATT
2582337 TATTA
1 TATTA
2582342 TATATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TATTAAAAATAAATATAAAAATAATT
Found at i:2582959 original size:11 final size:11
Alignment explanation
Indices: 2582943--2582978 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
2582933 GAGAACAAAT
*
2582943 TTCTCTCTGGC
1 TTCTCTCTAGC
2582954 TTCTCTCTAGC
1 TTCTCTCTAGC
2582965 TTCTCTCTAGC
1 TTCTCTCTAGC
2582976 TTC
1 TTC
2582979 CCTCATCGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.06, C:0.36, G:0.11, T:0.47
Consensus pattern (11 bp):
TTCTCTCTAGC
Found at i:2583660 original size:3 final size:3
Alignment explanation
Indices: 2583642--2583722 Score: 117
Period size: 3 Copynumber: 26.7 Consensus size: 3
2583632 TGTAATATTA
* *
2583642 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2583688 AAT TAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2583723 CATTAAAATG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2583985 original size:17 final size:17
Alignment explanation
Indices: 2583963--2584018 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2583953 TTGAATAAGC
2583963 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
* *
2583980 TCTTCTTCTCCTGATG-AGT
1 TCTTCTTAT--T-ATGAACT
*
2583999 TCTTCTCATTATGAACT
1 TCTTCTTATTATGAACT
2584016 TCT
1 TCT
2584019 CTGGGAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
19 10 0.33
20 3 0.10
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.50
Consensus pattern (17 bp):
TCTTCTTATTATGAACT
Found at i:2584183 original size:113 final size:112
Alignment explanation
Indices: 2583946--2584610 Score: 898
Period size: 113 Copynumber: 5.9 Consensus size: 112
2583936 TAGAGTCATT
* ** * * *
2583946 CAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
2584007 TTATGAACTTCTCTGGGAAAA-CTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTTCTCT-GGAAAAGCTGATCCATCAAGTGATAGATTTGAG
* * *
2584054 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
2584119 TTATGAAC-TCGAACTGGAAAAGAT-AGTCCATCAAGTGATAGATTTGAA
66 TTATGAACTTC--TCTGGAAAAGCTGA-TCCATCAAGTGATAGATTTGAG
*
2584167 CAAAAGGTTGAACAAATTCTTCTCGTTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTC
*** * *
2584232 TCATTATGAAC-TCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTAAG
63 TCATTATGAACTTCT--CTGGAAAAGCTGATCCATCAAGTGATAGATTTGAG
*
2584283 CAAAAGGTTGAACAAATTCTTCTGATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* ** *
2584348 TTATGAAC-TCGAACTGGAAAATATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTTC--TCTGGAAAAGCTGATCCATCAAGTGATAGATTTGAG
*
2584396 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
2584461 TTATGAACTTCTCTGGAAAAGCTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGATAGATTTGAG
* *
2584508 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
2584573 TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGAT
66 TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGAT
2584611 GAATTTAAAT
Statistics
Matches: 499, Mismatches: 41, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
108 31 0.06
109 1 0.00
111 3 0.01
112 164 0.33
113 194 0.39
114 4 0.01
115 2 0.00
116 99 0.20
117 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGATAGATTTGAG
Found at i:2584305 original size:229 final size:224
Alignment explanation
Indices: 2583946--2584610 Score: 977
Period size: 229 Copynumber: 3.0 Consensus size: 224
2583936 TAGAGTCATT
* ** * * *
2583946 CAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTC-T--TC-TTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
2584007 TTATGAACTTCTCTGGGAAAACTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATT
66 TTATGAACTTCTCT-GGAAAACTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATT
*
2584072 CTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
2584137 AAAGATAGTCCATCAAGTGATAGATTTGAA
195 AAAGATAGTCCATCAAGTGATAGATTTGAA
* *
2584167 CAAAAGGTTGAACAAATTCTTCTCGTTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTC-AG--ATGAGTTCTTC
** * * * * *
2584232 TCATTATGAAC-TCTACCTGGAAATTTTAATCCATCAAGTGATAGATTTAAGCAAAAGGTTGAAC
63 TCATTATGAACTTCT--CTGGAAA-ACTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAAC
* *
2584296 AAATTCTTCTGATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
125 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
* * *
2584361 CTGGAAAATATAATCCATCAAGTGATAGATTTGAG
190 CTGGAAAAGATAGTCCATCAAGTGATAGATTTGAA
2584396 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
2584461 TTATGAACTTCTCTGGAAAAGCTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAA-CTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATT
*
2584526 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC--TCTGG
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACTGG
*
2584589 AAAAGCT-GATCCATCAAGTGAT
194 AAAAGATAG-TCCATCAAGTGAT
2584611 GAATTTAAAT
Statistics
Matches: 395, Mismatches: 35, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
221 31 0.08
222 1 0.00
224 24 0.06
225 103 0.26
226 25 0.06
227 6 0.02
228 29 0.07
229 176 0.45
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (224 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAACTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
AAGATAGTCCATCAAGTGATAGATTTGAA
Found at i:2586753 original size:20 final size:19
Alignment explanation
Indices: 2586730--2586779 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 19
2586720 TGACCCCCCC
2586730 TTTTTCTTCTTTTTTCTCTT
1 TTTTTCTTCTTTTTTCT-TT
2586750 TTTTTCTTTTCTTTTTTCTTT
1 TTTTTC--TTCTTTTTTCTTT
2586771 TTTTTCTTC
1 TTTTTCTTC
2586780 AAACATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.11
20 6 0.21
21 8 0.29
22 11 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTCTTTTTTCTTT
Found at i:2586764 original size:22 final size:21
Alignment explanation
Indices: 2586736--2586778 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
2586726 CCCCTTTTTC
2586736 TTCTTTTTTCTCTTTTTTTCTT
1 TTCTTTTTTCT-TTTTTTTCTT
2586758 TTCTTTTTTCTTTTTTTTCTT
1 TTCTTTTTTCTTTTTTTTCTT
2586779 CAAACATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTCTTTTTTCTTTTTTTTCTT
Found at i:2594092 original size:15 final size:15
Alignment explanation
Indices: 2594069--2594100 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2594059 TGAAATGAAT
2594069 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2594084 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2594099 AA
1 AA
2594101 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2598142 original size:27 final size:26
Alignment explanation
Indices: 2598088--2598146 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2598078 TTTTCTTCGA
*
2598088 TATTGAAAAATAAATATTAAAATAATT
1 TATT-AAAAATAAATATAAAAATAATT
* *
2598115 TATTAAAAATATATATAAATAATTATT
1 TATTAAAAATAAATATAAA-AATAATT
2598142 TATTA
1 TATTA
2598147 TATATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TATTAAAAATAAATATAAAAATAATT
Found at i:2599451 original size:3 final size:3
Alignment explanation
Indices: 2599431--2599507 Score: 57
Period size: 3 Copynumber: 25.7 Consensus size: 3
2599421 TGTAATATTA
* * * * * * *
2599431 AAT AAT -AT ATAT ATT AAT AAT AAT TAT TAT TAT TAT TAT TAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2599476 TAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2599508 CATTAAAATG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (3 bp):
AAT
Found at i:2605523 original size:21 final size:21
Alignment explanation
Indices: 2605480--2605525 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2605470 CCGTTAAAAA
*
2605480 TTACCTAAAACATTATTTCTT
1 TTACCTAAAACATTATGTCTT
*
2605501 TTACCTAAAACATTAATGTTTT
1 TTACCTAAAACATT-ATGTCTT
2605523 TTA
1 TTA
2605526 ACATTTCCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (21 bp):
TTACCTAAAACATTATGTCTT
Found at i:2606333 original size:68 final size:66
Alignment explanation
Indices: 2606215--2606411 Score: 259
Period size: 68 Copynumber: 2.9 Consensus size: 66
2606205 AATTATGAAT
* * *
2606215 ATTACATAAATCTATTAAATAATATAATTTTCTAGAGATTCATTAGTTGATCAAGTGGTCAAGGA
1 ATTACATAAATCTATTAAATAATATAATTTTCTA-AGATACATTAATTGATCGAGTGGTCAAGGA
2606280 TG
65 TG
* * * * * *
2606282 ATTATATAAATCTATTCAAATAATTTAATTTTCTATAGATCCATTAATTGATTGAGTGGTTAATG
1 ATTACATAAATCTATT-AAATAATATAATTTTCTA-AGATACATTAATTGATCGAGTGGTCAAGG
2606347 ATG
64 ATG
* *
2606350 ATTACATAAATCTATTTAAATAATATAATTTTTTAAAATACATTAATTGATCGAGTGGTCAA
1 ATTACATAAATCTA-TTAAATAATATAATTTTCTAAGATACATTAATTGATCGAGTGGTCAA
2606412 TAATATTTAT
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 38 0.34
68 72 0.64
69 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (66 bp):
ATTACATAAATCTATTAAATAATATAATTTTCTAAGATACATTAATTGATCGAGTGGTCAAGGAT
G
Found at i:2615235 original size:2 final size:2
Alignment explanation
Indices: 2615228--2615261 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2615218 CCTTCTTGGA
2615228 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2615262 ATGTGGCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2624570 original size:14 final size:11
Alignment explanation
Indices: 2624539--2624568 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2624529 ATTAAGTCTC
2624539 AATTTTTAATA
1 AATTTTTAATA
2624550 AATTTTTAATA
1 AATTTTTAATA
2624561 ATATTTTT
1 A-ATTTTT
2624569 TTTCTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTTAATA
Found at i:2624854 original size:377 final size:377
Alignment explanation
Indices: 2624160--2624918 Score: 1367
Period size: 377 Copynumber: 2.0 Consensus size: 377
2624150 ATTATTTGTA
* * *
2624160 TCAATTTTTAATAAGTTTTTAATAATATTTTTTTTCTAAAGATTATAGAGCTGGGTATACGTACT
1 TCAATTTTTAATAAATTTTTAATAATATTTTTTTTCTAAAGAGTATAGAGATGGGTATACGTACT
*
2624225 ACCCGGCCGTTTAGCCTGTGGGTTTTGACGGTGCGAGCTTAAACGGAGCGATTTAAAAAACCTGC
66 ACCCGGCCGTTTAGCCTGCGGGTTTTGACGGTGCGAGCTTAAACGGAGCGATTTAAAAAACCTGC
2624290 AATCATAAACGGTCTTGAATTCTAAGACCCGCGGGCTAACGGGCTTACCCGCGACCCGTTAAATA
131 AATCATAAACGGTCTTGAATTCTAAGACCCGCGGGCTAACGGGCTTACCCGCGACCCGTTAAATA
*
2624355 ACAACAATTTTAAATGCTTTAAATGCAATAAAAATAATATTCTAACTTGCTACACCTTTAAAAAT
196 ACAACAATTTTAAATGCTTTAAATGCAATAAAAATAATATTCTAACATGCTACACCTTTAAAAAT
* *
2624420 GATCCAGCAACTTGAAAAGTCCATTATATTATTAAGTCTCAAGATAAACAAGTAAATAAATAACA
261 GATCCAGCAACTTGAAAAGTCCATTACACTATTAAGTCTCAAGATAAACAAGTAAATAAATAACA
2624485 CCATAATACCATTAAATCTCAATAAGTCTAAAATAAATAACACCATTAAGTC
326 CCATAATACCATTAAATCTCAATAAGTCTAAAATAAATAACACCATTAAGTC
2624537 TCAATTTTTAATAAATTTTTAATAATATTTTTTTTCTAAAGAGTATAGAGATGGGTATACGTACT
1 TCAATTTTTAATAAATTTTTAATAATATTTTTTTTCTAAAGAGTATAGAGATGGGTATACGTACT
* * *
2624602 ACCCGTCCGTTTAGTCC-GCGGGTTTTGACGGTGCGGGCTTAAACGGAGCGGTTTAAAAAACCTG
66 ACCCGGCCGTTTAG-CCTGCGGGTTTTGACGGTGCGAGCTTAAACGGAGCGATTTAAAAAACCTG
*
2624666 CAATCATAAACGGTCTTGAATTCTAAGACTCGCGGGCTAACGGGCTTACCCGCGACCCGTTAAAT
130 CAATCATAAACGGTCTTGAATTCTAAGACCCGCGGGCTAACGGGCTTACCCGCGACCCGTTAAAT
*
2624731 AACAACAATTTTAAATGCTTTAAATGCAATAAAAATAATGTTCTAACATGCTACACCTTTAAAAA
195 AACAACAATTTTAAATGCTTTAAATGCAATAAAAATAATATTCTAACATGCTACACCTTTAAAAA
*
2624796 TGATCCAGCAACTTGAAAAGTCCATTACACTATTAAGTCTTAAGATAAACAAGTAAATAAATAAC
260 TGATCCAGCAACTTGAAAAGTCCATTACACTATTAAGTCTCAAGATAAACAAGTAAATAAATAAC
* *
2624861 ACCATAATATCATTAAGTCTCAATAAGTCTAAAATAAATAACACCATTAAGTC
325 ACCATAATACCATTAAATCTCAATAAGTCTAAAATAAATAACACCATTAAGTC
2624914 TCAAT
1 TCAAT
2624919 AAGTCTAAAA
Statistics
Matches: 366, Mismatches: 15, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
377 364 0.99
378 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.30
Consensus pattern (377 bp):
TCAATTTTTAATAAATTTTTAATAATATTTTTTTTCTAAAGAGTATAGAGATGGGTATACGTACT
ACCCGGCCGTTTAGCCTGCGGGTTTTGACGGTGCGAGCTTAAACGGAGCGATTTAAAAAACCTGC
AATCATAAACGGTCTTGAATTCTAAGACCCGCGGGCTAACGGGCTTACCCGCGACCCGTTAAATA
ACAACAATTTTAAATGCTTTAAATGCAATAAAAATAATATTCTAACATGCTACACCTTTAAAAAT
GATCCAGCAACTTGAAAAGTCCATTACACTATTAAGTCTCAAGATAAACAAGTAAATAAATAACA
CCATAATACCATTAAATCTCAATAAGTCTAAAATAAATAACACCATTAAGTC
Found at i:2624902 original size:42 final size:39
Alignment explanation
Indices: 2624850--2624946 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 39
2624840 ATAAACAAGT
2624850 AAATAAATAACACCATAATATCATTAAGTCTCAATAAGTCTA
1 AAATAAATAACACCAT-A-A-CATTAAGTCTCAATAAGTCTA
2624892 AAATAAATAACA-C----CATTAAGTCTCAATAAGTCTA
1 AAATAAATAACACCATAACATTAAGTCTCAATAAGTCTA
*
2624926 AAATAAAAAAACACCATAACA
1 AAAT-AAATAACACCATAACA
2624947 CTAATAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
34 25 0.52
35 7 0.15
36 1 0.02
40 2 0.04
41 1 0.02
42 12 0.25
ACGTcount: A:0.55, C:0.18, G:0.04, T:0.24
Consensus pattern (39 bp):
AAATAAATAACACCATAACATTAAGTCTCAATAAGTCTA
Found at i:2624914 original size:34 final size:35
Alignment explanation
Indices: 2624871--2624942 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 35
2624861 ACCATAATAT
*
2624871 CATTAAGTCTCAATAAGTCTAAAAT-AAATAACAC
1 CATTAAGTCTCAATAAGTCTAAAATAAAAAAACAC
2624905 CATTAAGTCTCAATAAGTCTAAAATAAAAAAACAC
1 CATTAAGTCTCAATAAGTCTAAAATAAAAAAACAC
2624940 CAT
1 CAT
2624943 AACACTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 25 0.69
35 11 0.31
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.25
Consensus pattern (35 bp):
CATTAAGTCTCAATAAGTCTAAAATAAAAAAACAC
Found at i:2625766 original size:20 final size:21
Alignment explanation
Indices: 2625727--2625766 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2625717 GAACGAGAGA
2625727 ATTCAATTTGTGCTTCACAAT
1 ATTCAATTTGTGCTTCACAAT
*
2625748 ATTCAATTT-TGCTTGACAA
1 ATTCAATTTGTGCTTCACAA
2625767 GAAATTGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (21 bp):
ATTCAATTTGTGCTTCACAAT
Found at i:2630584 original size:20 final size:20
Alignment explanation
Indices: 2630556--2630594 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2630546 TTCATGAATG
*
2630556 GGTCAACGCAAGCGTAATCT
1 GGTCAACGCAAGCGCAATCT
*
2630576 GGTCGACGCAAGCGCAATC
1 GGTCAACGCAAGCGCAATC
2630595 CGGGCTGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (20 bp):
GGTCAACGCAAGCGCAATCT
Found at i:2633722 original size:16 final size:17
Alignment explanation
Indices: 2633701--2633733 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2633691 GTTTATAAGT
2633701 GAAATT-TATTTTATAC
1 GAAATTATATTTTATAC
2633717 GAAATTGATATTTTATA
1 GAAATT-ATATTTTATA
2633734 AAAGTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
GAAATTATATTTTATAC
Found at i:2634958 original size:23 final size:23
Alignment explanation
Indices: 2634929--2634973 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2634919 AGTGTTATAT
2634929 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
2634952 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
2634974 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:2634979 original size:23 final size:23
Alignment explanation
Indices: 2634930--2634998 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
2634920 GTGTTATATT
* * **
2634930 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
2634953 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
2634976 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
2634999 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:2634992 original size:19 final size:19
Alignment explanation
Indices: 2634968--2635038 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
2634958 TTAAATATAT
*
2634968 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
2634987 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
2635006 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
2635026 TTATTAAATATAT
1 TTATTAAA-ATAT
2635039 ACAAAATTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:2635002 original size:34 final size:34
Alignment explanation
Indices: 2634923--2635002 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 34
2634913 AGTAATAGTG
2634923 TTATATT-ATATTTTAAAAATATTAATTAGTATA
1 TTATATTAATATTTTAAAAATATTAATTAGTATA
*
2634956 TT-T-TAAATATATTTATTAAAATATT-ATTAG-ATTA
1 TTATATTAATAT-TTTA--AAAATATTAATTAGTA-TA
2634990 TTATATTAATATT
1 TTATATTAATATT
2635003 AAATATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
31 1 0.03
32 5 0.13
33 7 0.18
34 9 0.24
35 10 0.26
36 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (34 bp):
TTATATTAATATTTTAAAAATATTAATTAGTATA
Found at i:2635138 original size:22 final size:23
Alignment explanation
Indices: 2635110--2635188 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 23
2635100 TTGATTATTT
2635110 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
2635132 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
* * * *
2635155 TA-AATATATTTTAAATATTTTAA
1 TATTATA-ATATTAAAAATATTAA
2635178 TATT-TAATATT
1 TATTATAATATT
2635189 TTGATAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
22 24 0.55
23 20 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:2635654 original size:15 final size:15
Alignment explanation
Indices: 2635634--2635699 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
2635624 TTTTGGAAAA
2635634 TGAATTACTAGAATT
1 TGAATTACTAGAATT
*
2635649 TGAATTACTGGAATT
1 TGAATTACTAGAATT
* **
2635664 TTAATTACTTA-AAAA
1 TGAATTAC-TAGAATT
* *
2635679 TGAATTATTGGAATT
1 TGAATTACTAGAATT
2635694 TGAATT
1 TGAATT
2635700 CAGGAAAATG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
14 1 0.03
15 37 0.95
16 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (15 bp):
TGAATTACTAGAATT
Found at i:2635937 original size:27 final size:28
Alignment explanation
Indices: 2635902--2635957 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
2635892 TTTATCATAA
2635902 AAAATTAATATTA-TTATT-TTAAAATATT
1 AAAATTAAT-TTATTTATTATT-AAATATT
2635930 AAAA-TAATTTATTTATTATTAAATATT
1 AAAATTAATTTATTTATTATTAAATATT
2635957 A
1 A
2635958 TTTTTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.12
27 17 0.65
28 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAATTAATTTATTTATTATTAAATATT
Found at i:2636098 original size:23 final size:23
Alignment explanation
Indices: 2636049--2636099 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2636039 GTGATATATT
**
2636049 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
2636072 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
2636095 ATATT
1 ATATT
2636100 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:2636111 original size:19 final size:19
Alignment explanation
Indices: 2636087--2636157 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
2636077 TTAAATATCT
*
2636087 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
2636106 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
2636125 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
2636145 TTATTAAATATAT
1 TTATTAAA-ATAT
2636158 ACAAAATTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:2636251 original size:21 final size:21
Alignment explanation
Indices: 2636227--2636267 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2636217 ATTAATTATT
2636227 TATTATAATATTAAAAATATA
1 TATTATAATATTAAAAATATA
* *
2636248 TATTATATTATTATAAATAT
1 TATTATAATATTAAAAATAT
2636268 TAATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTATAATATTAAAAATATA
Found at i:2636253 original size:24 final size:22
Alignment explanation
Indices: 2636200--2636253 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
2636190 ATATAATATC
*
2636200 TTATATTATTATAATAAATTAA
1 TTATATTATTATAATAAATAAA
2636222 TTAT-TTATTATAATATTAA-AAA
1 TTATATTATTATAATA--AATAAA
2636244 TATATATTAT
1 T-TATATTAT
2636254 ATTATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 11 0.41
22 7 0.26
23 5 0.19
24 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATTATTATAATAAATAAA
Found at i:2636254 original size:50 final size:48
Alignment explanation
Indices: 2636173--2636271 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 48
2636163 ATTTATTATA
2636173 TATTTATTAAAATAAAAATATAATATCTTATATTATTATAATAAATTAAT
1 TATTTATTAAAATAAAAATATAATA-CTTATATTATTATAA-AAATTAAT
*
2636223 TATTTATTATAATATTAAAAATAT-ATA-TTATATTATTATAAATATTAAT
1 TATTTATTA-AA-A-TAAAAATATAATACTTATATTATTATAAAAATTAAT
2636272 AAATATATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
49 7 0.16
50 23 0.51
51 2 0.04
52 4 0.09
53 9 0.20
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (48 bp):
TATTTATTAAAATAAAAATATAATACTTATATTATTATAAAAATTAAT
Found at i:2636259 original size:33 final size:30
Alignment explanation
Indices: 2636211--2636302 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
2636201 TATATTATTA
*
2636211 TAATAAAT-TA-ATTATTTATTAT-AATAT
1 TAATAAATATATATTAATTATTATAAATAT
2636238 TAA-AAATATATATTATATTATTATAAATAT
1 TAATAAATATATATTA-ATTATTATAAATAT
* * *
2636268 TAATAAATATATTTTAAATATT-TTAATATT
1 TAATAAATATATATTAATTATTATAAATA-T
2636298 TAATA
1 TAATA
2636303 TTTTGATGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.07
27 5 0.09
28 4 0.07
29 12 0.22
30 19 0.35
31 11 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TAATAAATATATATTAATTATTATAAATAT
Found at i:2636280 original size:21 final size:21
Alignment explanation
Indices: 2636234--2636289 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2636224 ATTTATTATA
* * *
2636234 ATATTAAAAATATATATTATAT
1 ATATTATAAATAT-TAATAAAT
2636256 -TATTATAAATATTAATAAAT
1 ATATTATAAATATTAATAAAT
*
2636276 ATATTTTAAATATT
1 ATATTATAAATATT
2636290 TTAATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:2636559 original size:42 final size:43
Alignment explanation
Indices: 2636503--2636594 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 43
2636493 TTCCTCCAAC
* *
2636503 CAAACAC-TGGAAAACATTTTTCGGAAAACGTATTACGTGAAA
1 CAAACACGTGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
*
2636545 CAAACACGT-GAAAACATTTTCCGGAAAATGAATTACGTGAAA
1 CAAACACGTGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
2636587 CAAACACG
1 CAAACACG
2636595 AGATTTCGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (43 bp):
CAAACACGTGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
Found at i:2636869 original size:14 final size:15
Alignment explanation
Indices: 2636786--2636874 Score: 65
Period size: 15 Copynumber: 6.0 Consensus size: 15
2636776 TTAGTTTTCT
2636786 GGAAAATGAATTACTA
1 GGAAAATGAATTAC-A
** *
2636802 -GAATTTGAATTACT
1 GGAAAATGAATTACA
** * *
2636816 GGAATTTTAATTACT
1 GGAAAATGAATTACA
*
2636831 GAAAAATGAATTACA
1 GGAAAATGAATTACA
**
2636846 GGAATTTGAATT-CA
1 GGAAAATGAATTACA
2636860 GGAAAATGAATTACA
1 GGAAAATGAATTACA
2636875 TTTCTGGAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
14 12 0.21
15 45 0.79
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (15 bp):
GGAAAATGAATTACA
Found at i:2636874 original size:29 final size:30
Alignment explanation
Indices: 2636807--2636874 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
2636797 TACTAGAATT
* * *
2636807 TGAATTACTGGAATTTTAATTACTGAAAAA
1 TGAATTACAGGAATTTGAATTACAGAAAAA
*
2636837 TGAATTACAGGAATTTGAATT-CAGGAAAA
1 TGAATTACAGGAATTTGAATTACAGAAAAA
2636866 TGAATTACA
1 TGAATTACA
2636875 TTTCTGGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.32
Consensus pattern (30 bp):
TGAATTACAGGAATTTGAATTACAGAAAAA
Found at i:2637266 original size:17 final size:18
Alignment explanation
Indices: 2637244--2637311 Score: 52
Period size: 19 Copynumber: 3.8 Consensus size: 18
2637234 TTAAATATCT
*
2637244 TTATTA-AATATATTAGA
1 TTATTATAATATATTAAA
*
2637261 TTATTATATTAATATTAAA
1 TTATTATAAT-ATATTAAA
* *
2637280 TATATAATAATATTATT-CA
1 T-TATTATAATA-TATTAAA
2637299 TTATTA-AATATAT
1 TTATTATAATATAT
2637312 ACAAAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 3 0.07
17 10 0.24
18 6 0.15
19 11 0.27
20 11 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (18 bp):
TTATTATAATATATTAAA
Found at i:2637276 original size:28 final size:27
Alignment explanation
Indices: 2637245--2637312 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
2637235 TAAATATCTT
* * *
2637245 TATTAAATATATTAGATTATTATATTAA
1 TATTAAATATATAAGAATATTAT-TCAA
* *
2637273 TATTAAATATATAATAATATTATTCAT
1 TATTAAATATATAAGAATATTATTCAA
2637300 TATTAAATATATA
1 TATTAAATATATA
2637313 CAAAATTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTAAATATATAAGAATATTATTCAA
Found at i:2637322 original size:27 final size:27
Alignment explanation
Indices: 2637267--2637331 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
2637257 TAGATTATTA
*
2637267 TATTA-ATATTAAATATATAATAATAT
1 TATTATATATTAAATATATAAAAATAT
2637293 TATTCAT-TATTAAATATATACAAAAT-T
1 TATT-ATATATTAAATATATA-AAAATAT
2637320 TATTATATATTA
1 TATTATATATTA
2637332 TTAAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 6 0.18
27 24 0.71
28 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (27 bp):
TATTATATATTAAATATATAAAAATAT
Found at i:2637357 original size:54 final size:56
Alignment explanation
Indices: 2637237--2637368 Score: 130
Period size: 55 Copynumber: 2.3 Consensus size: 56
2637227 GTATATTTTA
* * *
2637237 AATATCTTTATTAAATATATTAGATTATTATATTAATATTAAATATATAATAATAT
1 AATATCATTATTAAATATATAAAATTATTATATTAATATTAAATATATAATAATAT
* *
2637293 TAT-TCATTATTAAATATATACAAAATTTATTATA-TATTATTAAA-ATA-AA-AATAT
1 AATATCATTATTAAATATAT--AAAA-TTATTATATTAATATTAAATATATAATAATAT
2637347 AATATCTTATTATTATAATATA
1 AATATC--ATTATTA-AATATA
2637369 ATTGATTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
54 7 0.11
55 19 0.30
56 5 0.08
57 18 0.29
58 14 0.22
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (56 bp):
AATATCATTATTAAATATATAAAATTATTATATTAATATTAAATATATAATAATAT
Found at i:2637418 original size:19 final size:17
Alignment explanation
Indices: 2637383--2637424 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
2637373 ATTATTTTAT
2637383 TATAT-TTAAAATATAA
1 TATATATTAAAATATAA
2637399 TATATATTATAAATATTAA
1 TATATATTA-AAATA-TAA
*
2637418 TAAATAT
1 TATATAT
2637425 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 5 0.23
19 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATATTAAAATATAA
Found at i:2637436 original size:8 final size:8
Alignment explanation
Indices: 2637423--2637452 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2637413 ATTAATAAAT
2637423 ATATTTTA
1 ATATTTTA
2637431 ATATTTTA
1 ATATTTTA
2637439 ATA-TTTA
1 ATATTTTA
2637446 ATATTTT
1 ATATTTT
2637453 GATGAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATATTTTA
Found at i:2637439 original size:22 final size:22
Alignment explanation
Indices: 2637395--2637441 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2637385 TATTTAAAAT
2637395 ATAATATATATTATAAATATTA
1 ATAATATATATTATAAATATTA
* *
2637417 ATAA-ATATATTTTAATATTTTA
1 ATAATATATATTATAA-ATATTA
2637439 ATA
1 ATA
2637442 TTTAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATATATTATAAATATTA
Found at i:2637696 original size:42 final size:42
Alignment explanation
Indices: 2637649--2637740 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
2637639 TTCCTCCAAC
* * * *
2637649 CAAACACTGAAAAACATTTTATGGAAAACGTATTACGTGAAA
1 CAAACACGGAAAAACATTTTACGAAAAACGAATTACGTGAAA
* * *
2637691 CAAACACGGGAAAACATTTTCCGAAAAATGAATTACGTGAAA
1 CAAACACGGAAAAACATTTTACGAAAAACGAATTACGTGAAA
2637733 CAAACACG
1 CAAACACG
2637741 AGATTTCGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (42 bp):
CAAACACGGAAAAACATTTTACGAAAAACGAATTACGTGAAA
Found at i:2644519 original size:46 final size:46
Alignment explanation
Indices: 2644461--2644561 Score: 193
Period size: 46 Copynumber: 2.2 Consensus size: 46
2644451 GATCAGGGGT
2644461 CGCGCTATACGCCGTACCAAAATTATATTTAACGCGGTCTCTGATC
1 CGCGCTATACGCCGTACCAAAATTATATTTAACGCGGTCTCTGATC
*
2644507 CGCGTTATACGCCGTACCAAAATTATATTTAACGCGGTCTCTGATC
1 CGCGCTATACGCCGTACCAAAATTATATTTAACGCGGTCTCTGATC
2644553 CGCGCTATA
1 CGCGCTATA
2644562 TAATAATTAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (46 bp):
CGCGCTATACGCCGTACCAAAATTATATTTAACGCGGTCTCTGATC
Found at i:2645208 original size:111 final size:111
Alignment explanation
Indices: 2645063--2645284 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
2645053 ATTACAAAAA
* *
2645063 TTAATTCTTACTCTAATAATTATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
2645128 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
2645174 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2645239 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
2645285 ATGATTTCTA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2645429 original size:20 final size:20
Alignment explanation
Indices: 2645406--2645447 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2645396 TATACCTTGA
2645406 AAATATAGA-ATATTTGAGAG
1 AAATATAGAGAT-TTTGAGAG
*
2645426 AAATTTAGAGATTTTGAGAG
1 AAATATAGAGATTTTGAGAG
2645446 AA
1 AA
2645448 TTTGATGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (20 bp):
AAATATAGAGATTTTGAGAG
Found at i:2662423 original size:18 final size:18
Alignment explanation
Indices: 2662400--2662436 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2662390 CCCTAGGCTA
*
2662400 ATATAAATAGGTTTTAAT
1 ATATAAATAGGTGTTAAT
*
2662418 ATATAAATGGGTGTTAAT
1 ATATAAATAGGTGTTAAT
2662436 A
1 A
2662437 AGGTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (18 bp):
ATATAAATAGGTGTTAAT
Found at i:2667806 original size:50 final size:50
Alignment explanation
Indices: 2667674--2667812 Score: 174
Period size: 49 Copynumber: 2.8 Consensus size: 50
2667664 TTTCTACGTC
* * * *
2667674 TATTAAAATAAGTTTTTAGTGTTCCATACTATCGCAACTAGATCCACTTA
1 TATTAAAATAAGTTTTTAGTCTTACATACTATTGCAAATAGATCCACTTA
* * * *
2667724 TATT-AAATAAGTTATCAGCCTTACA-AGCTATTGCAAATAGATCCACTTG
1 TATTAAAATAAGTTTTTAGTCTTACATA-CTATTGCAAATAGATCCACTTA
*
2667773 TATTAAAATAAGTTTTTAGTCTTATATACTATTGCAAATA
1 TATTAAAATAAGTTTTTAGTCTTACATACTATTGCAAATA
2667813 CATTCGATTT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 1 0.01
49 39 0.53
50 33 0.45
51 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (50 bp):
TATTAAAATAAGTTTTTAGTCTTACATACTATTGCAAATAGATCCACTTA
Found at i:2668415 original size:22 final size:22
Alignment explanation
Indices: 2668364--2668421 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
2668354 TTAAAAATTT
* *
2668364 AAAAACAATAAAAAAAATAAAT
1 AAAAACAATAAATAAAATAAAG
* *
2668386 ATACACAAT-AATAAAATAAAGG
1 AAAAACAATAAATAAAATAAA-G
*
2668408 AAAAACAATGAATA
1 AAAAACAATAAATA
2668422 TAGACGGTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 10 0.36
22 14 0.50
23 4 0.14
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAAACAATAAATAAAATAAAG
Found at i:2668590 original size:18 final size:18
Alignment explanation
Indices: 2668567--2668617 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2668557 TTAAAACTAT
2668567 AATTTAAAATTTTCTAAA
1 AATTTAAAATTTTCTAAA
*
2668585 AATTTAAAACTTATCTAAA
1 AATTTAAAA-TTTTCTAAA
**
2668604 TTTTTAAAAATTTT
1 AATTT-AAAATTTT
2668618 TGATGGAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.33
19 14 0.52
20 4 0.15
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTAAAATTTTCTAAA
Found at i:2668612 original size:19 final size:18
Alignment explanation
Indices: 2668567--2668603 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2668557 TTAAAACTAT
*
2668567 AATTTAAAATTTTCTAAA
1 AATTTAAAATTATCTAAA
2668585 AATTTAAAACTTATCTAAA
1 AATTTAAAA-TTATCTAAA
2668604 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAAAATTATCTAAA
Found at i:2676859 original size:30 final size:30
Alignment explanation
Indices: 2676823--2676920 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
2676813 CCCGAAAGAC
2676823 CTATCCAGAGGTCACAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
2676853 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
* * * * * *
2676883 CTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AA
2676914 CTATCCA
1 CTATCCA
2676921 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
30 50 0.86
31 8 0.14
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAA
Found at i:2677001 original size:32 final size:31
Alignment explanation
Indices: 2676878--2677009 Score: 119
Period size: 31 Copynumber: 4.3 Consensus size: 31
2676868 AAAGATCCTC
* * * * *
2676878 GGTA-ACTGTCCATAGGTCCCGAAGAACCTA
1 GGTATACTGTCCATATGTTCTGTAGAACATA
* *
2676908 GGTAAACTATCCATATGTTCCT-TAGAACATA
1 GGTATACTGTCCATATGTT-CTGTAGAACATA
*
2676939 GGTATACTGTCCATATG-TCTCG-AAAGACATA
1 GGTATACTGTCCATATGTTCT-GTAGA-ACATA
*
2676970 GGTAGTTCTGTCCATATGTTCTGTAGAACATA
1 GGTA-TACTGTCCATATGTTCTGTAGAACATA
2677002 GGTATACT
1 GGTATACT
2677010 CTCGACTCTT
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.02
30 7 0.09
31 45 0.55
32 23 0.28
33 5 0.06
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCTGTAGAACATA
Found at i:2678111 original size:23 final size:23
Alignment explanation
Indices: 2678085--2678171 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
2678075 CAGCTCATAT
2678085 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCGCGTAG
* *** *
2678108 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGGAGTGCCGCGT-AG
2678132 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCGCGTAG
*
2678155 AATTGCACCGTAGTGCC
1 AATTGCACCGGAGTGCC
2678172 ATATAATAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 34 0.65
24 18 0.35
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCGCGTAG
Found at i:2678140 original size:24 final size:24
Alignment explanation
Indices: 2678108--2678181 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
2678098 TGCCGCGTAG
2678108 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGTAGTGCCATATAAT
* *** *
2678132 AATTGCACCGGAGTGCCGCGT-AG
1 AATTGCACCGTAGTGCCATATAAT
2678155 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGTAGTGCCATATAAT
2678179 AAT
1 AAT
2678182 GTCCATAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AATTGCACCGTAGTGCCATATAAT
Found at i:2678146 original size:47 final size:47
Alignment explanation
Indices: 2678083--2678181 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
2678073 CACAGCTCAT
2678083 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
2678130 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
2678177 ATAAT
1 ATAAT
2678182 GTCCATAAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (47 bp):
ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
Found at i:2678359 original size:103 final size:103
Alignment explanation
Indices: 2678180--2678405 Score: 393
Period size: 103 Copynumber: 2.2 Consensus size: 103
2678170 CCATATAATA
* *
2678180 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
2678244 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
2678283 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
2678348 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
2678386 ATGTCCCGAAA-GACCACATA
1 ATGTCCC-AAAGGACCACATA
2678406 GACCCTCGAC
Statistics
Matches: 118, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
103 112 0.95
104 6 0.05
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:2683915 original size:23 final size:23
Alignment explanation
Indices: 2683889--2683975 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
2683879 CAGCTCATAT
2683889 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACCGGAGTGCCGTGTAG
* * * *
2683912 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGGAGTGCCGTGT-AG
*
2683936 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCGTGTAG
*
2683959 AATTGCACCGTAGTGCC
1 AATTGCACCGGAGTGCC
2683976 ATATAATAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 35 0.66
24 18 0.34
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCGTGTAG
Found at i:2683950 original size:47 final size:47
Alignment explanation
Indices: 2683887--2683985 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
2683877 CACAGCTCAT
*
2683887 ATAATTGCACCGGAGTGCCGTGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
2683934 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
2683981 ATAAT
1 ATAAT
2683986 GTCCATAAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (47 bp):
ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
Found at i:2684163 original size:103 final size:103
Alignment explanation
Indices: 2683984--2684209 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
2683974 CCATATAATA
* **
2683984 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGT
2684048 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
2684087 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTG
2684152 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
2684190 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
2684210 GACCCTCGAC
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 114 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:2698129 original size:15 final size:16
Alignment explanation
Indices: 2698097--2698129 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2698087 TAAATCTTTC
2698097 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
2698113 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
2698128 TT
1 TT
2698130 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:2698903 original size:16 final size:16
Alignment explanation
Indices: 2698879--2698912 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2698869 TATCGCCGAC
*
2698879 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2698895 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2698911 CG
1 CG
2698913 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2715923 original size:10 final size:10
Alignment explanation
Indices: 2715908--2715932 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2715898 GCCATTGATC
2715908 AACAACAAGA
1 AACAACAAGA
2715918 AACAACAAGA
1 AACAACAAGA
2715928 AACAA
1 AACAA
2715933 GAATCAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:2717971 original size:258 final size:256
Alignment explanation
Indices: 2717633--2718148 Score: 978
Period size: 258 Copynumber: 2.0 Consensus size: 256
2717623 TTATTATTCA
*
2717633 TATTGAACCTGATATGTTGCTGCTTTGATTCTGTTATTCTGTAGTACTACTTTTAAGTCAAATTT
1 TATTGAACCTGATATGTTGCTGCTTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
*
2717698 TGTAGGTATGCTACTGCGCTAGAGAGAAACCCAGAAGATTATGATTCTCTTTACAACTGGGCATT
66 TGTAGGTATGCTACTGCGCTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGCATT
2717763 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATGATATTGTTATCTTAACATCATTCAAAATGATA
131 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATGATATTGTTATCTTAACATCATTC--AATGATA
*
2717828 TATCATGTCCAATTCTTATTTTGCTAGAACTTCCTGCTTAAGTTTATGAATGTAAACATGATG
194 TATCATGTCCAATTCTTATTTTGCTAGAACTTCCTGCTTAAGTTTATGAAAGTAAACATGATG
2717891 TATTGAACCTGATATGTTGCTGCTTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
1 TATTGAACCTGATATGTTGCTGCTTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
*
2717956 TGTAGGTATGCTACTGCGCTAGAGAGAAACCCATAAGATTATGATGCTCTTTACAACTGGGCATT
66 TGTAGGTATGCTACTGCGCTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGCATT
2718021 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATGATATTGTTATCTTAACATCATTCAATGATATA
131 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATGATATTGTTATCTTAACATCATTCAATGATATA
2718086 TCATGTCCAATTCTTATTTTGCTAGAACTTCCTGCTTAAGTTTATGAAAGTAAACATGATG
196 TCATGTCCAATTCTTATTTTGCTAGAACTTCCTGCTTAAGTTTATGAAAGTAAACATGATG
2718147 TA
1 TA
2718149 ATCTTTGCAA
Statistics
Matches: 254, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
256 71 0.28
258 183 0.72
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (256 bp):
TATTGAACCTGATATGTTGCTGCTTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
TGTAGGTATGCTACTGCGCTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGCATT
GGTTCTTCAAGTTTGAGATGCTGGTTCATTATGATATTGTTATCTTAACATCATTCAATGATATA
TCATGTCCAATTCTTATTTTGCTAGAACTTCCTGCTTAAGTTTATGAAAGTAAACATGATG
Found at i:2718481 original size:56 final size:56
Alignment explanation
Indices: 2718395--2718517 Score: 194
Period size: 56 Copynumber: 2.2 Consensus size: 56
2718385 GATGACTTCT
* *
2718395 CAGAATGCATAAGCCATATAAGAAGCTGGATAGACAAG-AAAATAAGTGTGGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAGAAAAATAAGTGT-AAGATG
*
2718451 CAGAATGCATAAGCTATATAAAAAGCTGGATAGACAAGAAAAATAAGTGTAAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAGAAAAATAAGTGTAAGATG
*
2718507 CATAATGCATA
1 CAGAATGCATA
2718518 GATGTTCCCA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 51 0.82
57 11 0.18
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.20
Consensus pattern (56 bp):
CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAGAAAAATAAGTGTAAGATG
Found at i:2719968 original size:24 final size:26
Alignment explanation
Indices: 2719932--2719991 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
2719922 TAAAAGATAA
2719932 ATAATAAATTATTATATATAGA-AGAT
1 ATAATAAATTATTATAT-TAGATAGAT
2719958 ATAAT-AA-TATTATATTAGATAGAT
1 ATAATAAATTATTATATTAGATAGAT
*
2719982 AATAAAAAAT
1 -ATAATAAAT
2719992 AATTTACATC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 12 0.41
25 6 0.21
26 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (26 bp):
ATAATAAATTATTATATTAGATAGAT
Found at i:2726827 original size:30 final size:30
Alignment explanation
Indices: 2726789--2726928 Score: 163
Period size: 30 Copynumber: 4.6 Consensus size: 30
2726779 GTCTGCATAT
*
2726789 TAATAATTCTGCTCATATTAATTTTGCTTG
1 TAATAATTCTGCTCATATTAATTCTGCTTG
* *
2726819 TGATAATTCTGCTCGTATTAATTCTGCTTG
1 TAATAATTCTGCTCATATTAATTCTGCTTG
**
2726849 TAATAATTCTGCTCATATTAATTCTGCTCA
1 TAATAATTCTGCTCATATTAATTCTGCTTG
* ** *
2726879 TATTAATTCTGCTTGTAATAATTCTGCTTG
1 TAATAATTCTGCTCATATTAATTCTGCTTG
*
2726909 TATTGATAATGCTGCTCATA
1 TA---ATAATTCTGCTCATA
2726929 ATTTTTTGCC
Statistics
Matches: 90, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
30 79 0.88
33 11 0.12
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (30 bp):
TAATAATTCTGCTCATATTAATTCTGCTTG
Found at i:2726845 original size:45 final size:45
Alignment explanation
Indices: 2726792--2726912 Score: 163
Period size: 45 Copynumber: 2.7 Consensus size: 45
2726782 TGCATATTAA
** * * *
2726792 TAATTCTGCTCATATTAATTTTGCTTGTGA-TAATTCTGCTCGTAT
1 TAATTCTGCTTGTAATAATTCTGCTTGT-ATTAATTCTGCTCATAT
**
2726837 TAATTCTGCTTGTAATAATTCTGCTCATATTAATTCTGCTCATAT
1 TAATTCTGCTTGTAATAATTCTGCTTGTATTAATTCTGCTCATAT
2726882 TAATTCTGCTTGTAATAATTCTGCTTGTATT
1 TAATTCTGCTTGTAATAATTCTGCTTGTATT
2726913 GATAATGCTG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
44 1 0.02
45 65 0.98
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (45 bp):
TAATTCTGCTTGTAATAATTCTGCTTGTATTAATTCTGCTCATAT
Found at i:2726910 original size:15 final size:15
Alignment explanation
Indices: 2726789--2726906 Score: 128
Period size: 15 Copynumber: 7.9 Consensus size: 15
2726779 GTCTGCATAT
*
2726789 TAATAATTCTGCTCA
1 TAATAATTCTGCTCG
* * *
2726804 TATTAATTTTGCTTG
1 TAATAATTCTGCTCG
*
2726819 TGATAATTCTGCTCG
1 TAATAATTCTGCTCG
* *
2726834 TATTAATTCTGCTTG
1 TAATAATTCTGCTCG
*
2726849 TAATAATTCTGCTCA
1 TAATAATTCTGCTCG
* *
2726864 TATTAATTCTGCTCA
1 TAATAATTCTGCTCG
* *
2726879 TATTAATTCTGCTTG
1 TAATAATTCTGCTCG
2726894 TAATAATTCTGCT
1 TAATAATTCTGCT
2726907 TGTATTGATA
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 85 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (15 bp):
TAATAATTCTGCTCG
Found at i:2728222 original size:18 final size:18
Alignment explanation
Indices: 2728173--2728225 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2728163 TTCACAACTA
* *
2728173 CTACATCACTACAACCAT
1 CTACATCACTACCATCAT
*
2728191 CTTCAT--CT-CCATCAT
1 CTACATCACTACCATCAT
2728206 CTACATCACTACCATCAT
1 CTACATCACTACCATCAT
2728224 CT
1 CT
2728226 TCTCCATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 2 0.07
18 14 0.50
ACGTcount: A:0.30, C:0.40, G:0.00, T:0.30
Consensus pattern (18 bp):
CTACATCACTACCATCAT
Found at i:2728237 original size:6 final size:6
Alignment explanation
Indices: 2728226--2728329 Score: 68
Period size: 6 Copynumber: 16.3 Consensus size: 6
2728216 ACCATCATCT
* * *
2728226 TCTCCA TCTCCA TCTCCA TCATCTA -CGTCACTA CCACCA TCTCCA TCTCCA
1 TCTCCA TCTCCA TCTCCA TC-TCCA TC-TC-C-A TCTCCA TCTCCA TCTCCA
* * *
2728277 TCTCCA TCATCTACA TCACTA -CTACTA TCTCCA TCTCCA TCTCCA TCTCCA
1 TCTCCA TC-TC--CA TCTCCA TCT-CCA TCTCCA TCTCCA TCTCCA TCTCCA
2728328 TC
1 TC
2728330 ACCACCACCA
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
5 1 0.01
6 62 0.78
7 8 0.10
8 3 0.04
9 5 0.06
ACGTcount: A:0.22, C:0.45, G:0.01, T:0.32
Consensus pattern (6 bp):
TCTCCA
Found at i:2728238 original size:18 final size:18
Alignment explanation
Indices: 2728193--2728294 Score: 57
Period size: 18 Copynumber: 6.2 Consensus size: 18
2728183 ACAACCATCT
2728193 TCATCTCCATCATCTACA
1 TCATCTCCATCATCTACA
*
2728211 TCA-CTACCATCATCTTC-
1 TCATCT-CCATCATCTACA
2728228 TCCATCTCCATC-TC--CA
1 T-CATCTCCATCATCTACA
* *
2728244 TCATCTACGTCA-CTACCA
1 TCATCTCCATCATCTA-CA
*
2728262 CCATCT-C--CATCT-C-
1 TCATCTCCATCATCTACA
2728275 -CATCTCCATCATCTACA
1 TCATCTCCATCATCTACA
2728292 TCA
1 TCA
2728295 CTACTACTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 30
0.66 0.04 0.30
Matches are distributed among these distances:
12 5 0.08
13 1 0.02
14 1 0.02
15 17 0.26
16 4 0.06
17 6 0.09
18 29 0.45
19 2 0.03
ACGTcount: A:0.25, C:0.43, G:0.01, T:0.31
Consensus pattern (18 bp):
TCATCTCCATCATCTACA
Found at i:2728280 original size:45 final size:44
Alignment explanation
Indices: 2728187--2728329 Score: 170
Period size: 45 Copynumber: 3.2 Consensus size: 44
2728177 ATCACTACAA
* *
2728187 CCATCTTCATCTCCATCATCTACATCACTACCATCATCT---TCT
1 CCATCTCCATCTCCATCATCTAC-TCACTACCACCATCTCCATCT
2728229 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCT
1 CCATCTCCATCTCCATCATCTAC-TCACTACCACCATCTCCATCT
* *
2728274 CCATCTCCATCATCTACATCA-CTACT-ACTATCTCCATCTCCATCT
1 CCATCTCCATC-TC--CATCATCTACTCACTACCACCATCTCCATCT
2728319 CCATCTCCATC
1 CCATCTCCATC
2728330 ACCACCACCA
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
42 36 0.40
45 42 0.47
46 3 0.03
47 4 0.04
48 5 0.06
ACGTcount: A:0.23, C:0.44, G:0.01, T:0.32
Consensus pattern (44 bp):
CCATCTCCATCTCCATCATCTACTCACTACCACCATCTCCATCT
Found at i:2728330 original size:45 final size:39
Alignment explanation
Indices: 2728187--2728339 Score: 204
Period size: 39 Copynumber: 3.9 Consensus size: 39
2728177 ATCACTACAA
* *
2728187 CCATCTTCATCTCCATCATCTACATCACTACCATCATCTTCT
1 CCATCTCCATCTCCATCATCTACATCACTACCA-C--CATCT
*
2728229 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCT
1 CCATCTCCATCTCCATCATCTACATCACTACCACCATCT
* *
2728268 CCATCTCCATCTCCATCATCTACATCACTACTACTATCT
1 CCATCTCCATCTCCATCATCTACATCACTACCACCATCT
*
2728307 CCATCTCCATCTCCATC-TC--CATCACCACCACCA
1 CCATCTCCATCTCCATCATCTACATCACTACCACCA
2728340 CCTGTCACGA
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
36 11 0.11
38 2 0.02
39 57 0.56
41 1 0.01
42 31 0.30
ACGTcount: A:0.24, C:0.45, G:0.01, T:0.30
Consensus pattern (39 bp):
CCATCTCCATCTCCATCATCTACATCACTACCACCATCT
Found at i:2730120 original size:13 final size:13
Alignment explanation
Indices: 2730102--2730127 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2730092 AAGCTTGAGC
2730102 AGTTGGGCTAGTT
1 AGTTGGGCTAGTT
2730115 AGTTGGGCTAGTT
1 AGTTGGGCTAGTT
2730128 GTTATATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
AGTTGGGCTAGTT
Done.